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The Seven Bridges Platform is a simple solution for doing bioinformatics at industrial scale. But sometimes, everyone needs a little help.

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Platform documentation

GET STARTED

About the Seven Bridges Platform
- Time synchronization
Before you start
QuickStart
Account settings
About the Payments page
Manage your subscription
Cloud infrastructure pricing
Developer Dashboard
Email notifications page

TUTORIALS

Seven Bridges Platform tutorials
Build a workflow tutorial
Worked example of uploading SAMtools Sort
Upload a custom python program using a Dockerfile
Create a tar archive
Troubleshooting tutorial

ACCESS THE SEVEN BRIDGES PLATFORM

Sign up for the Seven Bridges Platform
Access via the visual interface
Access via the API
Set up two-factor authentication

MANAGE AN ANALYSIS ENVIRONMENT

Projects on the Seven Bridges Platform
Create a project
View a project
Manage the project dashboard
Modify project settings
Manage email notifications
Add notes to your project
Leave a project
Delete a project
Tag your projects

COLLABORATE SECURELY

Collaboration on the Seven Bridges Platform
Add a collaborator to a project
Set permissions

DATASETS HUB

About datasets
About metadata for datasets
Query datasets via the Data Browser
Querying multiple datasets
Access data from datasets
About the Datasets API

BRING YOUR PRIVATE DATA

Upload your data to the Seven Bridges Platform
Upload from your computer
Upload via the command line
Upload via the Seven Bridges Platform Uploader
Import from an FTP/HTTP(S) server
Upload via the API
Import from a Volume

SET METADATA ASSOCIATED WITH A FILE

Metadata on the Seven Bridges Platform
Set metadata using the visual interface
Set metadata using the command line uploader
Set metadata using the API
Format of a manifest file
Modify metadata using the visual interface

SEARCH FILES

File repositories on the Seven Bridges Platform
Search files on the Platform

ADD FILES TO A PROJECT

Copy files using the visual interface
Copy files using the API
Tag your files

ORGANIZE FILES

Available actions

ARCHIVE FILES (on AWS)

File archiving overview
Archive a file
Restore a file
Delete an archived file

ARCHIVE APPS

App archiving overview
Archive an app
Restore an app

SBFS (Beta)

About SBFS
Install SBFS automatically
Install SBFS manually
Configure SBFS credentials
List available projects for SBFS
Mount a project
Unmount a project
Command reference
SBFS Log
Upgrade SBFS
Uninstall SBFS

FIND APPS

Apps on the Seven Bridges Platform
Search for an app
Explore app details
App versions

BRING YOUR TOOLS

About the SDK
About the Common Workflow Language
CWL v.1.0 improvements over sbg:draft-2

DOCKER

About Docker
Install Docker
Image registries
- About the Seven Bridges Image Registry
- About Docker Hub
Create and upload a Docker image
Create and upload a Docker image with a Dockerfile
Manage Docker repositories
Core Docker commands
Docker for Enterprise
Mount a USB drive in a Docker container

DESCRIBE YOUR TOOL (LEGACY)

The Tool Editor
General tool information
Tool input ports
Tool output ports
Additional tool information
Test the tool description
Dynamic Expressions in Tool Descriptions
Advanced features of the tool editor
Forking tools

TOOL WRAPPING TIPS AND TRICKS

Tips and tricks

COPY AN APP

Copy public apps to a project
Copy an app from a project

EDIT AN APP (LEGACY)

Edit a tool
Create a workflow
Edit a workflow
Add revision notes

Edit an app

About the editor
The tool editor
The workflow editor

RUN AN ANALYSIS

About analyses
About batch analyses
Run a task
Define app settings
Set computation instances

TASK EXECUTION

About task execution
About controlling task execution
About parallelizing tool executions
About tool resource requirements
About Memoization (WorkReuse)
Project and file locations
Set execution hints at workflow level
Set execution hints at node level
Set execution hints at tool level
Set execution hints at task level
About Spot Instances
Use Spot Instances
List of execution hints
List of task statuses
List of available Amazon Web Services US instances
List of available Amazon Web Services EU instances

REVIEW A TASK

Review the task page
View task stats
View task logs
Job retry
View instance metrics
Real-time job monitoring
Troubleshoot a failed task

VIEW ANALYSIS RESULTS

View output files

INTERACTIVE ANALYSIS

Interactive analysis on the Platform
Seven Bridges Genome Browser
Variant Browser
VCF Benchmarking app
CummeRbundQC RNA-Seq Visualization
FastQC
Picard Collect Alignment Summary Metrics
The Seven Bridges Coverage app

RHEO

Overview
Manage via CLI
Manage via API
Manage via RHEO visual interface (GUI)
RHEO glossary

RHEO FOR DEVELOPERS

Overview
RHEO Developer tutorial
Create automations for the RHEO visual interface (GUI)
- Automation inputs
- Automation outputs

GRAPH GENOME APPS

About Graph Genome apps
Graph WGS
- About Graph WGS
- Graph Germline Variant Detection Workflow tutorial

DATA CRUNCHER

About Data Cruncher
JupyterLab quick reference
RStudio quick reference
Run a Data Cruncher analysis
Data Cruncher analysis details
Copy a Data Cruncher analysis
Data Cruncher analysis charging
Data Cruncher analysis editor
Data Cruncher environments and libraries

DOWNLOAD RESULTS

Download results

DEVELOPER TOOLS

Developer Hub
Get your authentication token
Publish your app in the Public Apps gallery
Integrate your web application

PUBLIC PROJECTS

Public projects overview
Smart Variant Filtering
Data Cruncher Interactive Analyses
VCF Benchmarking
Cancer Cell Line Encyclopedia (CCLE)
Simons Genome Diversity Project (SGDP) dataset
Human Cell Atlas Preview Datasets

ENTERPRISE FEATURES

About the Enterprise feature
Collaboration within an Enterprise
Manage an Enterprise
Manage a Division
Add a collaborator to an Enterprise project
Switch between Divisions
Manage two-factor authentication
Manage Docker repositories

API Hub

API Overview
API tutorials
API rate limit
Using volumes via the API

API CLIENTS

API Clients
Store credentials to access Seven Bridges client applications and libraries
R library
Python library recipes
Python library
Java library
Java library Quickstart
Seven Bridges Command Line Interface
Seven Bridges Command Line Interface Reference

Connect cloud storage

Connect cloud storage overview
Volumes
Aliases
Supported cloud storage providers
Amazon Web Services Simple Storage Service (AWS S3) Volumes
Google Cloud Storage (GCS) Volumes
Security concerns when working with volumes
Enabling cross-origin resource sharing (CORS)
Operations on volumes
API Cloud storage tutorials
- AWS Cloud storage tutorial
- Google Cloud Storage tutorial

GLOSSARY

Glossary

GET STARTED

About the Seven Bridges Platform
- Time synchronization
Before you start
QuickStart
Account settings
About the Payments page
Manage your subscription
Cloud infrastructure pricing
Developer Dashboard
Email notifications page

TUTORIALS

Seven Bridges Platform tutorials
Build a workflow tutorial
Worked example of uploading SAMtools Sort
Upload a custom python program using a Dockerfile
Create a tar archive
Troubleshooting tutorial

ACCESS THE SEVEN BRIDGES PLATFORM

Sign up for the Seven Bridges Platform
Access via the visual interface
Access via the API
Set up two-factor authentication

MANAGE AN ANALYSIS ENVIRONMENT

Projects on the Seven Bridges Platform
Create a project
View a project
Manage the project dashboard
Modify project settings
Manage email notifications
Add notes to your project
Leave a project
Delete a project
Tag your projects

COLLABORATE SECURELY

Collaboration on the Seven Bridges Platform
Add a collaborator to a project
Set permissions

DATASETS HUB

About datasets
About metadata for datasets
Query datasets via the Data Browser
Querying multiple datasets
Access data from datasets
About the Datasets API

BRING YOUR PRIVATE DATA

Upload your data to the Seven Bridges Platform
Upload from your computer
Upload via the command line
Upload via the Seven Bridges Platform Uploader
Import from an FTP/HTTP(S) server
Upload via the API
Import from a Volume

SET METADATA ASSOCIATED WITH A FILE

Metadata on the Seven Bridges Platform
Set metadata using the visual interface
Set metadata using the command line uploader
Set metadata using the API
Format of a manifest file
Modify metadata using the visual interface

SEARCH FILES

File repositories on the Seven Bridges Platform
Search files on the Platform

ADD FILES TO A PROJECT

Copy files using the visual interface
Copy files using the API
Tag your files

ORGANIZE FILES

Available actions

ARCHIVE FILES (on AWS)

File archiving overview
Archive a file
Restore a file
Delete an archived file

ARCHIVE APPS

App archiving overview
Archive an app
Restore an app

SBFS (Beta)

About SBFS
Install SBFS automatically
Install SBFS manually
Configure SBFS credentials
List available projects for SBFS
Mount a project
Unmount a project
Command reference
SBFS Log
Upgrade SBFS
Uninstall SBFS

FIND APPS

Apps on the Seven Bridges Platform
Search for an app
Explore app details
App versions

BRING YOUR TOOLS

About the SDK
About the Common Workflow Language
CWL v.1.0 improvements over sbg:draft-2

DOCKER

About Docker
Install Docker
Image registries
- About the Seven Bridges Image Registry
- About Docker Hub
Create and upload a Docker image
Create and upload a Docker image with a Dockerfile
Manage Docker repositories
Core Docker commands
Docker for Enterprise
Mount a USB drive in a Docker container

DESCRIBE YOUR TOOL (LEGACY)

The Tool Editor
General tool information
Tool input ports
Tool output ports
Additional tool information
Test the tool description
Dynamic Expressions in Tool Descriptions
Advanced features of the tool editor
Forking tools

TOOL WRAPPING TIPS AND TRICKS

Tips and tricks

COPY AN APP

Copy public apps to a project
Copy an app from a project

EDIT AN APP (LEGACY)

Edit a tool
Create a workflow
Edit a workflow
Add revision notes

Edit an app

About the editor
The tool editor
The workflow editor

RUN AN ANALYSIS

About analyses
About batch analyses
Run a task
Define app settings
Set computation instances

TASK EXECUTION

About task execution
About controlling task execution
About parallelizing tool executions
About tool resource requirements
About Memoization (WorkReuse)
Project and file locations
Set execution hints at workflow level
Set execution hints at node level
Set execution hints at tool level
Set execution hints at task level
About Spot Instances
Use Spot Instances
List of execution hints
List of task statuses
List of available Amazon Web Services US instances
List of available Amazon Web Services EU instances

REVIEW A TASK

Review the task page
View task stats
View task logs
Job retry
View instance metrics
Real-time job monitoring
Troubleshoot a failed task

VIEW ANALYSIS RESULTS

View output files

INTERACTIVE ANALYSIS

Interactive analysis on the Platform
Seven Bridges Genome Browser
Variant Browser
VCF Benchmarking app
CummeRbundQC RNA-Seq Visualization
FastQC
Picard Collect Alignment Summary Metrics
The Seven Bridges Coverage app

RHEO

Overview
Manage via CLI
Manage via API
Manage via RHEO visual interface (GUI)
RHEO glossary

RHEO FOR DEVELOPERS

Overview
RHEO Developer tutorial
Create automations for the RHEO visual interface (GUI)
- Automation inputs
- Automation outputs

GRAPH GENOME APPS

About Graph Genome apps
Graph WGS
- About Graph WGS
- Graph Germline Variant Detection Workflow tutorial

DATA CRUNCHER

About Data Cruncher
JupyterLab quick reference
RStudio quick reference
Run a Data Cruncher analysis
Data Cruncher analysis details
Copy a Data Cruncher analysis
Data Cruncher analysis charging
Data Cruncher analysis editor
Data Cruncher environments and libraries

DOWNLOAD RESULTS

Download results

DEVELOPER TOOLS

Developer Hub
Get your authentication token
Publish your app in the Public Apps gallery
Integrate your web application

PUBLIC PROJECTS

Public projects overview
Smart Variant Filtering
Data Cruncher Interactive Analyses
VCF Benchmarking
Cancer Cell Line Encyclopedia (CCLE)
Simons Genome Diversity Project (SGDP) dataset
Human Cell Atlas Preview Datasets

ENTERPRISE FEATURES

About the Enterprise feature
Collaboration within an Enterprise
Manage an Enterprise
Manage a Division
Add a collaborator to an Enterprise project
Switch between Divisions
Manage two-factor authentication
Manage Docker repositories

API Hub

API Overview
API tutorials
API rate limit
Using volumes via the API

API CLIENTS

API Clients
Store credentials to access Seven Bridges client applications and libraries
R library
Python library recipes
Python library
Java library
Java library Quickstart
Seven Bridges Command Line Interface
Seven Bridges Command Line Interface Reference

Connect cloud storage

Connect cloud storage overview
Volumes
Aliases
Supported cloud storage providers
Amazon Web Services Simple Storage Service (AWS S3) Volumes
Google Cloud Storage (GCS) Volumes
Security concerns when working with volumes
Enabling cross-origin resource sharing (CORS)
Operations on volumes
API Cloud storage tutorials
- AWS Cloud storage tutorial
- Google Cloud Storage tutorial

GLOSSARY

Glossary

API Reference

Return all paths
- List all API paths
User
- Get my information
Users
- List user resources
Billing
Projects
Files, folders and metadata
Upload files
Apps
Tasks
Volumes
Actions
- Send a feedback item
Rate Limit
- Get your current rate limit status
API status codes

Markers API (Advance Access)

About the Markers API
List markers available on a file
Get details for a single marker
Create a marker
Modify a single marker
Delete a single marker

ENTERPRISE API

Enterprise features overview
List all your divisions
List division members
Remove a division member
Get details of a division
List all your teams in a division
Get details of a team
Create a team
Add a team member
List team members
Rename a team
Delete a team
Remove a team member

BULK ACTIONS

Bulk features overview
Start a bulk import job
Get details of a bulk import job
Start a bulk export job
Get details of a bulk export job
Bulk deletion of files
Get details of multiple files
Update details of multiple files
Edit details of multiple files
Get details of multiple tasks

ASYNC BULK ACTIONS

Overview
Copy multiple files
Delete multiple files and folders
Get details of a copy job
Get details of a deletion job
Get details of all async jobs
Move multiple files or folders
Get details of a move job

RHEO automations

Managing automations overview
List all automations
Create a new automation
Edit an automation
Add a code package to an automation
Get details of an automation
List members of an automation
Add an automation member
Add a team to an automation (Enterprise)
Get an automation member's permissions
Modify automation member's permissions
Remove an automation member
List all automation code packages
Get details of an automation code package
List all automation runs
Create a new automation run
Re-run an automation
Get details of an automation run
Stop an automation
Get content of the automation state file
Archive an automation
Restore an automation
Archive a code package
Restore a code package
Access an automation log file
Edit an automation run
Edit an automation entity
List multipart code package uploads
Get details of a multipart upload
Get upload URL for a part
Initialize a multipart code package upload
Complete a multipart code package upload
Report an uploaded part
Report uploaded parts
Abort a multipart code package upload

Tips and tricks

Contents

Make files available in your tool's working directory
Set the default value for an input port
JavaScript Cookbook

Updated 2 years ago

Table of Contents

Contents

Tips and tricks

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Any Questions?

If you don't find an answer to your question, please get in touch. Send us a message at [email protected] or contact @sbgenomics on Twitter.

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